Gromacs Import Warning

[angeyx]

Hi, I installed gromacs wrapper after installing Gromacs. But when I tried import gromacs in jupyter lab, it gave me a warning

c:\users\carno\appdata\local\programs\python\python38\lib\site-packages\gromacs\__init__.py:286: GromacsImportWarning: Some Gromacs commands were NOT found; maybe source GMXRC first? The following are missing: ['release']
I also couldn't call any gromacs tools. When I open the .gromacswrapper.cfg, release, gmrx, and tools are all empty, which I don't think is normal.

Any ideas on how to solve this? I'm new to gromacs and using Win10 system & gromacs-2022.3. Happy to provide more information if needed.

[orbeckst]

The warning really says that GromacsWrapper could not find your gmx executable on your PATH. I don't have a windows machine so I can't test things directly. Ultimately, this is a question about configuration but before I can suggest anything specific, let me ask a few questions:

1. How did you install GromacsWrapper?
2. How did you install GROMACS?
3. Where is GROMACS installed?
4. Can you open a terminal (also known as command line or shell) and work there?
5. How do you launch Jupyter?

[angeyx]

1. I installed GromacsWrapper via both pip and conda install. The above error is when I launched it through the command prompt. A similar error will happen if I launch Jupyter through the anaconda prompt.
2. I installed GROMACS via Ubuntu
3. it was installed it in c:\users\carno\
4. If I directly run python and import gromacs in the command prompt, it will give the same error, if that is what you're asking.

[orbeckst]

How do you run gmx from the command line?

What is the full path of the gmx executable?

[angeyx]

I was trying to trouble-shoot GROMACS these few days. I seem to have two versions installed at two places.

• one at /usr/bin/gmx , version 2020.10 Ubuntu-2020.1-1., (I think I installed accidentally following a tutorial, directly via Ubuntu apt install gromacs) . I can run this directly via Ubuntu.
• one at usr/local/gromacs/bin/gmx, version gmx, 2022.3 (I downloaded the package from GROMACS and followed the instructions). I have to source it first before running.

I probably need to remove one of them and go with one.

[angeyx]

Hi an update -- I figured it out. I think the problem is the windows and Linux/WSL environments. I installed Anaconda for windows prior to I installed Ubuntu, and used it to install gromacswrapper and run my code. gromacswrapper has trouble finding my gmx because they reside in different file systems, so even when I modify the GMXRC=... in the config file, it can't find/access it. Now I installed Anaconda for Linux from Ubuntu, and then installed gromacswrapper, and it worked finally! Thanks for pointing out the PATH problem -- that points me in the right direction.

[orbeckst]

Glad that you figured it out!

…

Am 10/8/22 um 13:42 schrieb angeyx ***@***.***>:  Hi an update -- I figured it out. I think the problem is the windows and Linux/WSL environments. I installed Anaconda for windows prior to I installed Ubuntu, and used it to install gromacswrapper and run my code. gromacswrapper has trouble finding my gmx because they reside in different file systems, so even when I modify the GMXRC=... in the config file, it can't find/access it. Now I installed Anaconda for Linux from Ubuntu, and then installed gromacswrapper, and it worked finally! Thanks for pointing out the PATH problem -- that points me in the right direction. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.